PUZZLE 4.0.2 Type of analysis: tree reconstruction Parameter estimation: approximate (faster) Parameter estimation uses: neighbor-joining tree (for substitution process and rate variation) Standard errors (S.E.) are obtained by the curvature method. The upper and lower bounds of an approximate 95% confidence interval for parameter or branch length x are x-1.96*S.E. and x+1.96*S.E. SEQUENCE ALIGNMENT Input data: 11 sequences with 3165 nucleotide sites Number of constant sites: 9 (= 0.3% of all sites) SUBSTITUTION PROCESS Model of substitution: HKY (Hasegawa et al. 1985) Transition/transversion parameter (estimated from data set): 1.04 (S.E. 0.04) Nucleotide frequencies (estimated from data set): pi(A) = 25.5% pi(C) = 25.0% pi(G) = 24.6% pi(T) = 24.9% Expected transition/transversion ratio: 1.04 Expected pyrimidine transition/purine transition ratio: 1.00 RATE HETEROGENEITY Model of rate heterogeneity: uniform rate SEQUENCES IN INPUT ORDER 5% chi-square test p-value FROG passed 63.92% [2] FLOWER failed 0.00% [0] SOY failed 0.00% [4] HOMO passed 96.89% [1] PIG passed 77.20% [2] COW passed 78.49% [1] MOUSE failed 0.02% [3] RAT failed 0.72% [1] TROUT passed 6.68% [4] DANIO passed 67.54% [2] CELEGANS passed 33.08% [4] The chi-square tests compares the nucleotide composition of each sequence to the frequency distribution assumed in the maximum likelihood model. The number in square brackets indicates how often each sequence is involved in one of the 6 completely unresolved quartets of the quartet puzzling tree search. IDENTICAL SEQUENCES The sequences in each of the following groups are all identical. To speed up computation please remove all but one of each group from the data set. All sequences are unique. MAXIMUM LIKELIHOOD DISTANCES Maximum likelihood distances are computed using the selected model of substitution and rate heterogeneity. 11 FROG 0.00000 0.55665 0.57474 1.00148 0.88263 0.96207 0.94163 0.98540 0.63105 1.10313 1.03879 FLOWER 0.55665 0.00000 0.32956 0.58626 0.60469 0.58338 0.59717 0.59614 0.68086 0.64118 0.58617 SOY 0.57474 0.32956 0.00000 0.57092 0.58225 0.57137 0.58761 0.58465 0.61245 0.65485 0.64286 HOMO 1.00148 0.58626 0.57092 0.00000 0.17684 0.17162 0.20999 0.20945 0.42106 0.40028 0.45951 PIG 0.88263 0.60469 0.58225 0.17684 0.00000 0.11299 0.21458 0.21411 0.40630 0.42897 0.45491 COW 0.96207 0.58338 0.57137 0.17162 0.11299 0.00000 0.22778 0.22250 0.38836 0.41378 0.45756 MOUSE 0.94163 0.59717 0.58761 0.20999 0.21458 0.22778 0.00000 0.07529 0.41464 0.39061 0.44499 RAT 0.98540 0.59614 0.58465 0.20945 0.21411 0.22250 0.07529 0.00000 0.40655 0.39791 0.45587 TROUT 0.63105 0.68086 0.61245 0.42106 0.40630 0.38836 0.41464 0.40655 0.00000 0.38767 0.48097 DANIO 1.10313 0.64118 0.65485 0.40028 0.42897 0.41378 0.39061 0.39791 0.38767 0.00000 0.48437 CELEGANS 1.03879 0.58617 0.64286 0.45951 0.45491 0.45756 0.44499 0.45587 0.48097 0.48437 0.00000 Average distance (over all possible pairs of sequences): 0.51308 TREE SEARCH Quartet puzzling is used to choose from the possible tree topologies and to simultaneously infer support values for internal branches. Number of puzzling steps: 1000 Analysed quartets: 330 Unresolved quartets: 6 (= 1.8%) Quartet trees are based on approximate maximum likelihood values using the selected model of substitution and rate heterogeneity. QUARTET PUZZLING TREE Support for the internal branches of the unrooted quartet puzzling tree topology is shown in percent. This quartet puzzling tree is completely resolved. :---MOUSE :----100: : :---RAT :-98: : : :---PIG : : :-98: : :-97: :---COW :-79: : : : :-------HOMO : : :-98: : :---TROUT : : :---------88: : : :---DANIO :-89: : : : :-------------------CELEGANS : : : :-----------------------SOY : :---------------------------FLOWER : :---------------------------FROG Quartet puzzling tree (in CLUSTAL W notation): (FROG,(((((MOUSE,RAT)100,((PIG,COW)98,HOMO)97)98,(TROUT,DANIO)88)79, CELEGANS)98,SOY)89,FLOWER); BIPARTITIONS The following bipartitions occured at least once in all intermediate trees that have been generated in the 1000 puzzling steps: Bipartitions included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ******..** * : 1000 ***....... . : 981 ***.....** * : 978 ****..**** * : 976 ***...**** * : 971 **........ . : 894 ********.. * : 880 ***....... * : 790 Bipartitions not included in the quartet puzzling tree: (bipartition with sequences in input order : number of times seen) ***.....** . : 166 *..******* * : 106 ***.....*. . : 76 ***.....*. * : 72 ***.*.**** * : 22 ***.*...** * : 16 *..******* . : 14 ***.**..** * : 14 ********.. . : 12 ******.... * : 10 **.******* . : 5 ******..*. * : 5 ***...**.. * : 4 ***.**.... * : 2 ***...**** . : 2 *********. . : 2 ***.*..... * : 2 MAXIMUM LIKELIHOOD BRANCH LENGTHS ON QUARTET PUZZLING TREE (NO CLOCK) Branch lengths are computed using the selected model of substitution and rate heterogeneity. :-7 MOUSE :--12 : :-8 RAT :---15 : : :--5 PIG : : :--13 : : : :--6 COW : :--14 : :---4 HOMO :---17 : : :-----9 TROUT : :---16 : :-----10 DANIO :-------18 : :------11 CELEGANS :-19 : :----3 SOY : :----2 FLOWER : :----------1 FROG branch length S.E. branch length S.E. FROG 1 0.40168 0.03818 12 0.06243 0.00715 FLOWER 2 0.13716 0.01453 13 0.04651 0.00579 SOY 3 0.15297 0.01426 14 0.04154 0.00675 HOMO 4 0.09011 0.00724 15 0.10060 0.01240 PIG 5 0.05495 0.00557 16 0.08284 0.01463 COW 6 0.06077 0.00586 17 0.08650 0.01503 MOUSE 7 0.03706 0.00463 18 0.25310 0.02157 RAT 8 0.03991 0.00477 19 0.03557 0.01372 TROUT 9 0.19496 0.02371 DANIO 10 0.18059 0.01581 14 iterations until convergence CELEGANS 11 0.24470 0.02029 log L: -14998.68 Quartet puzzling tree with maximum likelihood branch lengths (in CLUSTAL W notation): (FROG:0.40168,(((((MOUSE:0.03706,RAT:0.03991)100:0.06243,((PIG:0.05495, COW:0.06077)98:0.04651,HOMO:0.09011)97:0.04154)98:0.10060,(TROUT:0.19496, DANIO:0.18059)88:0.08284)79:0.08650,CELEGANS:0.24470)98:0.25310, SOY:0.15297)89:0.03557,FLOWER:0.13716); TIME STAMP Date and time: Wed Jun 04 20:28:19 2003 Runtime: 12 seconds (= 0.2 minutes = 0.0 hours)